Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding (English)
National licence
- New search for: Lee, Michael S.
- New search for: Olson, Mark A.
- New search for: Lee, Michael S.
- New search for: Olson, Mark A.
In:
The Journal of Chemical Physics
;
134
, 24
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7
;
2011
- Article (Journal) / Electronic Resource
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Title:Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding
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Additional title:Adaptive replica exchange method comparison
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Contributors:Lee, Michael S. ( author ) / Olson, Mark A. ( author )
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Published in:The Journal of Chemical Physics ; 134, 24 ; 7
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Publisher:
- New search for: American Institute of Physics
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Publication date:2011-06-28
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Size:7 pages
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ISSN:
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DOI:
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Type of media:Article (Journal)
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Type of material:Electronic Resource
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Language:English
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Keywords:
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Source:
Table of contents – Volume 134, Issue 24
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
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Communication: Universality of the melting curves for a wide range of interaction potentialsKhrapak, Sergey A. / Chaudhuri, Manis / Morfill, Gregor E. et al. | 2011
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Communication: A new spectroscopic window on hydroxyl radicals using UV + VUV resonant ionizationBeames, Joseph M. / Liu, Fang / Lester, Marsha I. / Murray, Craig et al. | 2011
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Communication: Linear-expansion shooting techniques for accelerating self-consistent field convergenceWang, Yan Alexander / Yam, Chi Yung / Chen, Ya Kun / Chen, GuanHua et al. | 2011
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A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. I. General formalism and application to open-shell statesMiranda, R. P. / Fisher, A. J. / Stella, L. / Horsfield, A. P. et al. | 2011
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A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. II. Coulomb interaction effects in single conjugated polymer chainsMiranda, R. P. / Fisher, A. J. / Stella, L. / Horsfield, A. P. et al. | 2011
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Quantum effects in energy and charge transfer in an artificial photosynthetic complexGhosh, Pulak Kumar / Smirnov, Anatoly Yu. / Nori, Franco et al. | 2011
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A comparison of accelerators for direct energy minimization in electronic structure calculationsBaarman, Kurt / VandeVondele, Joost et al. | 2011
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Index k saddles and dividing surfaces in phase space with applications to isomerization dynamicsCollins, Peter / Ezra, Gregory S. / Wiggins, Stephen et al. | 2011
- 244106
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Pade´ spectrum decompositions of quantum distribution functions and optimal hierarchical equations of motion construction for quantum open systemsHu, Jie et al. | 2011
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Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperaturesChodera, John D. / Swope, William C. / Noé, Frank / Prinz, Jan-Hendrik / Shirts, Michael R. / Pande, Vijay S. et al. | 2011
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Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamicsPrinz, Jan-Hendrik / Chodera, John D. / Pande, Vijay S. / Swope, William C. / Smith, Jeremy C. / Noé, Frank et al. | 2011
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Ab initio study of excited state electronic circular dichroism. Two prototype cases: Methyl oxirane and R-(+)-1,1′-bi(2-naphthol)Rizzo, Antonio / Vahtras, Olav et al. | 2011
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Benchmark of density functional theory methods on the prediction of bond energies and bond distances of noble-gas containing moleculesLai, Tai-Yuan / Yang, Chun-Yu / Lin, Hsiao-Jing / Yang, Chang-Yu / Hu, Wei-Ping et al. | 2011
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Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-foldingLee, Michael S. / Olson, Mark A. et al. | 2011
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Analytical evaluation of first-order electrical properties based on the spin-free Dirac-Coulomb HamiltonianCheng, Lan / Gauss, Jürgen et al. | 2011
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Brueckner doubles coupled cluster method with the polarizable continuum model of solvationCaricato, Marco / Scalmani, Giovanni / Frisch, Michael J. et al. | 2011
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Decoherence and surface hopping: When can averaging over initial conditions help capture the effects of wave packet separation?Subotnik, Joseph E. / Shenvi, Neil et al. | 2011
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A general formulation for the efficient evaluation of n-electron integrals over products of Gaussian charge distributions with Gaussian geminal functionsKomornicki, Andrew / King, Harry F. et al. | 2011
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Mixed quantum-classical simulations of charge transport in organic materials: Numerical benchmark of the Su-Schrieffer-Heeger modelWang, Linjun / Beljonne, David / Chen, Liping / Shi, Qiang et al. | 2011
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Development and application of the analytical energy gradient for the normalized elimination of the small component methodZou, Wenli / Filatov, Michael / Cremer, Dieter et al. | 2011
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Optimizing transition interface sampling simulationsBorrero, Ernesto E. / Weinwurm, Marcus / Dellago, Christoph et al. | 2011
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Photoelectron imaging spectroscopy of nitroethane anionsAdams, Christopher L. / Weber, J. Mathias et al. | 2011
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Non-linear dynamics of the photodissociation of nitrous oxide: Equilibrium points, periodic orbits, and transition statesMauguiere, Frederic / Farantos, Stavros C. / Suarez, Jaime / Schinke, Reinhard et al. | 2011
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Gas phase solvatochromic effects of phenol and naphthol photoacidsMelnichuk, Anna / Bartlett, Rodney J. et al. | 2011
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Sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) of thiol and thioether compoundsBehyan, Shirin / Hu, Yongfeng / Urquhart, Stephen G. et al. | 2011
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The oxidation of Al atoms embedded in water clusters: A dynamical study of the relay (Grotthuss-like) mechanismÁlvarez-Barcia, S. / Flores, J. R. et al. | 2011
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Ultrafast internal conversion in ethylene. I. The excited state lifetimeTao, H. / Allison, T. K. / Wright, T. W. / Stooke, A. M. / Khurmi, C. / van Tilborg, J. / Liu, Y. / Falcone, R. W. / Belkacem, A. / Martinez, T. J. et al. | 2011
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A new “spectroscopic” potential energy surface for formaldehyde in its ground electronic stateYachmenev, Andrey / Yurchenko, Sergei N. / Jensen, Per / Thiel, Walter et al. | 2011
- 244308
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Axis-switching in the vibrationless A~←X~ transition of the jet-cooled deuterated methyl peroxy radical CD3O2Dupre´, Patrick et al. | 2011
- 244309
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Internal rotation: Single diagonalization approach versus standard approaches, application to the methyl peroxy radical A~←X~ transitionDupre´, Patrick et al. | 2011
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Cis-trans isomerization in the S1 state of acetylene: Identification of cis-well vibrational levelsMerer, Anthony J. / Steeves, Adam H. / Baraban, Joshua H. / Bechtel, Hans A. / Field, Robert W. et al. | 2011
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Reduced dimension discrete variable representation study of cis–trans isomerization in the S1 state of C2H2Baraban, J. H. / Beck, A. R. / Steeves, A. H. / Stanton, J. F. / Field, R. W. et al. | 2011
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Threshold photoelectron study of naphthalene, anthracene, pyrene, 1,2-dihydronaphthalene, and 9,10-dihydroanthraceneMayer, Paul M. / Blanchet, Valerie / Joblin, Christine et al. | 2011
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Infrared spectra and quantum chemical calculations of the uranium-carbon molecules UC, CUC, UCH, and U(CC)2Wang, Xuefeng / Andrews, Lester / Ma, Dongxia / Gagliardi, Laura / Gonçalves, António P. / Pereira, Cláudia C. L. / Marçalo, Joaquim / Godart, Claude / Villeroy, Benjamin et al. | 2011
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Confined water inside single-walled carbon nanotubes: Global phase diagram and effect of finite lengthKyakuno, Haruka / Matsuda, Kazuyuki / Yahiro, Hitomi / Inami, Yu / Fukuoka, Tomoko / Miyata, Yasumitsu / Yanagi, Kazuhiro / Maniwa, Yutaka / Kataura, Hiromichi / Saito, Takeshi et al. | 2011
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Terahertz spectrum and normal-mode relaxation in pentaerythritol tetranitrate: Effect of changes in bond-stretching force-field termsPereverzev, Andrey / Sewell, Thomas D. et al. | 2011
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Vibrationally quantum-state-specific dynamics of the reactions of CN radicals with organic molecules in solutionRose, Rebecca A. / Greaves, Stuart J. / Oliver, Thomas A. A. / Clark, Ian P. / Greetham, Gregory M. / Parker, Anthony W. / Towrie, Michael / Orr-Ewing, Andrew J. et al. | 2011
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Coinage metal (4, 4) nanotubes, simulated by first-principles calculationsFa, Wei / Zhou, Jian / Dong, Jinming / Kawazoe, Y. et al. | 2011
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Computer investigations on the asymptotic behavior of the rate coefficient for the annihilation reaction A + A → product and the trapping reaction in three dimensionsLitniewski, Marek / Gorecki, Jerzy et al. | 2011
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Brownian dynamics simulation of a model simple electrolyte in solvents of low dielectric constantYamaguchi, T. / Akatsuka, T. / Koda, S. et al. | 2011
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Intermolecular vibrations and fast relaxations in supercooled ionic liquidsRibeiro, Mauro C. C. et al. | 2011
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The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrodeCostanzo, Francesca / Sulpizi, Marialore / Valle, Raffaele Guido Della / Sprik, Michiel et al. | 2011
- 244509
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On the behavior of Bro-nsted-Evans-Polanyi relations for transition metal oxidesVojvodic, A. et al. | 2011
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Anomalies in supercooled NaCl aqueous solutions: A microscopic perspectiveLonginotti, M. Paula / Carignano, Marcelo A. / Szleifer, Igal / Corti, Horacio R. et al. | 2011
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Polarized Raman spectroscopic study on the solvent state of glassy LiCl aqueous solutions and the state of relaxed high-density amorphous icesSuzuki, Yoshiharu / Tominaga, Yasunori et al. | 2011
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Kinetic enhancement in nanoscale electrochemical systems caused by non-normal distributions of the electrode potentialGarcía-Morales, Vladimir / Krischer, Katharina et al. | 2011
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Effect of nanotube-length on the transport properties of single-file water molecules: Transition from bidirectional to unidirectionalSu, Jiaye / Guo, Hongxia et al. | 2011
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Ultrasoft primitive model of polyionic solutions: Structure, aggregation, and dynamicsCoslovich, Daniele / Hansen, Jean-Pierre / Kahl, Gerhard et al. | 2011
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Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachmentPadovan-Merhar, Olivia / Lara, Fernando Vargas / Starr, Francis W. et al. | 2011
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Reaction of aluminum clusters with waterOhmura, Satoshi / Shimojo, Fuyuki / Kalia, Rajiv K. / Kunaseth, Manaschai / Nakano, Aiichiro / Vashishta, Priya et al. | 2011
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Accuracy of existing atomic potentials for the CdTe semiconductor compoundWard, D. K. / Zhou, X. W. / Wong, B. M. / Doty, F. P. / Zimmerman, J. A. et al. | 2011
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Spin transport properties of single metallocene molecules attached to single-walled carbon nanotubes via nickel adatomsWei, Peng / Sun, Lili / Benassi, Enrico / Shen, Ziyong / Sanvito, Stefano / Hou, Shimin et al. | 2011
- 244705
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On the stability of "non-magic" endohedrally doped Si clusters: A first-principles sampling study of MSi16+ (MPalagin, Dennis et al. | 2011
-
Ion-erosion induced surface nanoporosity and nanotopography on SiSüle, P. et al. | 2011
-
Ab initio study of dielectric response of rippled grapheneSedelnikova, O. V. / Bulusheva, L. G. / Okotrub, A. V. et al. | 2011
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Effects of disordered interchain interactions on polaron dynamics in semiconducting polymersYuan, Xiao-Juan / Dong, Xian-Feng / Li, Dong-Mei / Liu, De-Sheng et al. | 2011
-
Three dimensional cross-correlation dynamic light scattering by non-ergodic turbid mediaHaro-Pérez, C. / Ojeda-Mendoza, G. J. / Rojas-Ochoa, L. F. et al. | 2011
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Rotational and translational self-diffusion in concentrated suspensions of permeable particlesAbade, Gustavo C. / Cichocki, Bogdan / Ekiel-Jeżewska, Maria L. / Nägele, Gerhard / Wajnryb, Eligiusz et al. | 2011
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Coil-to-globule transition by dissipative particle dynamics simulationGuo, Jiayi / Liang, Haojun / Wang, Zhen-Gang et al. | 2011
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Spectral collocation methods for polymer brushesChantawansri, Tanya L. / Hur, Su-Mi / García-Cervera, Carlos J. / Ceniceros, Hector D. / Fredrickson, Glenn H. et al. | 2011
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Conformational study of a single molecule of poly para phenylene ethynylenes in dilute solutionsMaskey, Sabina / Pierce, Flint / Perahia, Dvora / Grest, Gary S. et al. | 2011
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A semi-analytical description of protein folding that incorporates detailed geometrical informationSuzuki, Yoko / Noel, Jeffrey K. / Onuchic, José N. et al. | 2011
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Note: Perturbation theory of polymer chains revisited. I. Corrected C1 and C2 parameters for excluded volume chainsZifferer, Gerhard / Olaj, Oskar Friedrich et al. | 2011
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Comment on “Discussion on a mechanical equilibrium condition of a sessile drop on a smooth solid surface” [Ghasemi, H. / Ward, C. A. et al. | 2011
-
Internal rotation: Single diagonalization approach versus standard approaches, application to the methyl peroxy radical $\widetilde{\hspace*{-4pt}A}\leftarrow \widetilde{\hspace*{-2pt}X}$ transitionDupré, Patrick et al. | 2011
-
On the behavior of Brønsted-Evans-Polanyi relations for transition metal oxidesVojvodic, A. / Calle-Vallejo, F. / Guo, W. / Wang, S. / Toftelund, A. / Studt, F. / Martínez, J. I. / Shen, J. / Man, I. C. / Rossmeisl, J. et al. | 2011
-
Padé spectrum decompositions of quantum distribution functions and optimal hierarchical equations of motion construction for quantum open systemsHu, Jie / Luo, Meng / Jiang, Feng / Xu, Rui-Xue / Yan, YiJing et al. | 2011
-
Axis-switching in the vibrationless $\widetilde{A}\leftarrow \widetilde{X}$ transition of the jet-cooled deuterated methyl peroxy radical CD3O2Dupré, Patrick et al. | 2011
-
On the stability of “non-magic” endohedrally doped Si clusters: A first-principles sampling study of M${\rm Si}_{16}^+$ (M = Ti,V,Cr)Palagin, Dennis / Gramzow, Matthias / Reuter, Karsten et al. | 2011